Comparative NMR analysis of the decadeoxynucleotide d-(GCATTAATGC)₂and an anlogue containing 2-aminoadenine

Abstract

The dodecadeoxynucleotide duplex d-(GCATTAATGC)2 has been prepared with all adenine bases replaced by 2-NH2-adenine. This modified duplex has been characterized by nuclear magnetic resonance (NMR) spectroscopy. Complete sequence-specific 1H resonance assignments have been obtained by using a variety of 2D NMR methods. Multiple quantum-filtered and multiple quantum experiments have been used to completely assign all sugar ring protons, including 5'H and 5'H resonances. The assignments form the basis for a detailed comparative analysis of the 1H NMR parameters of the modified and parent duplex. The structural features of both decamer duplexes in solution are characteristic of the B-DNA family. The spin-spin coupling constants in the sugar rings and the relative spatial proximities of protons in the bases and sugars (as determined from the comparison of corresponding nuclear Overhauser effects) are virtually identical in the parent and modified duplexes. Thus, substitution by this adenine analogue in oligonucleotides appears not to disturb the global or local conformation of the DNA duplex.

E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA

“…Given the efficiency with which many restriction enzymes and Taq polymerases operate on DAP DNA [22, 23], the fact that TOP2A relaxes positive supercoils in normal and DAP DNA at similar rates, and the decreased wrapping of DAP DNA by gyrase, the failure to negative supercoil DAP DNA is unlikely to result from deformation of the DNA that impedes reversible cleavage and re-ligation of the gate segment. Indeed, short DAP-substituted DNA fragments appear to be undistorted, B-form DNA[20]. Instead, due to the increased stiffness of DAP DNA, gyrase likely fails to wrap the adjacent DAP DNA segment prior to strand passage.…”

“…This extra amino group is available for H-bonding with the electronegative oxygen atom on thymine to form a third H-bond between DAP and thymine. The melting temperature and the width of the minor groove at DAP:T base pairs are very similar to those of a G:C base pair [19], and NMR has shown that DAP-substituted, 10 bp-long DNA maintains the B-form [20]. However, the extra exocyclic amino groups of DAP:T base pairs are located in the DNA minor groove which may facilitate transitions to A- or Z-form helices [21].…”

Direct Real Time Observation of Base Flipping by theEcoRI DNA Methyltransferase

“…2). The 2,6-DAP:thymidine base pair (36,37), increases to three the number of hydrogen bonds to be broken during base pair disruption. These analogs (purine derivatives) form stable base pairs with the partner thymidine; therefore, the nearest neighbor stacking interactions are expected to remain relatively unperturbed (38).…”

High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA

“…The strategies for sequence-speci®c 1 H resonance assignments have been extensively reviewed (Wemmer & Reid, 1985;Wu È thrich, 1986;Reid, 1987;Patel et al, 1987a,b;van de Ven & Hilbers, 1988). We speci®cally used the protocols described by Chazin and co-workers (Chazin et al 1986(Chazin et al , 1991 for the ligand-free duplex, with a few modi®-cations for the DSA-DNA complex. Interproton distances are speci®ed using the short-hand notation of Wu È thrich (1986 H -endo-type sugar ring conformations.…”